PLINK v1.90b3z 64-bit (22 Nov 2015)
Options in effect:
  --bfile sNL4
  --geno 0.05
  --hwe 1e-4
  --maf 0.01
  --make-bed
  --mind 0.05
  --out sNL4_qc

Hostname: n0034.compute.hpc
Working directory: /hpc/hers_en/keijk/course
Start time: Wed Mar  2 15:24:29 2022

Random number seed: 1646231069
128722 MB RAM detected; reserving 64361 MB for main workspace.
711202 variants loaded from .bim file.
3488 people (1998 males, 1490 females) loaded from .fam.
3488 phenotype values loaded from .fam.
58 people removed due to missing genotype data (--mind).
IDs written to sNL4_qc.irem .
Using 1 thread (no multithreaded calculations invoked.
Before main variant filters, 3430 founders and 0 nonfounders present.
Calculating allele frequencies... done.
Warning: 614508 het. haploid genotypes present (see sNL4_qc.hh ); many commands
treat these as missing.
Warning: Nonmissing nonmale Y chromosome genotype(s) present; many commands
treat these as missing.
Total genotyping rate in remaining samples is 0.996398.
8951 variants removed due to missing genotype data (--geno).
Warning: --hwe observation counts vary by more than 10%.  Consider using
--geno, and/or applying different p-value thresholds to distinct subsets of
your data.
--hwe: 1957 variants removed due to Hardy-Weinberg exact test.
74302 variants removed due to minor allele threshold(s)
(--maf/--max-maf/--mac/--max-mac).
625992 variants and 3430 people pass filters and QC.
Among remaining phenotypes, 1216 are cases and 2214 are controls.
--make-bed to sNL4_qc.bed + sNL4_qc.bim + sNL4_qc.fam ... done.

End time: Wed Mar  2 15:24:42 2022